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Čermáková E, Mukherjee S, Nováková D, Horká P, Zdeňková K, Demnerová K. Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12788-12797. [PMID: 38778779 PMCID: PMC11157528 DOI: 10.1021/acs.jafc.4c01410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Fish from the pike (Esox) genus are valued in gastronomy for their superior meat quality. However, they can cause allergic reactions in sensitive consumers. This work aimed to fill the gap in the detection of pike allergens using molecular-biological techniques. New, fast, and accurate loop-mediated isothermal amplification (LAMP) and real-time PCR (qPCR) assays were designed to detect pike DNA using the parvalbumin gene as a marker. LAMP was assessed by electrophoresis, SYBR green optical detection, and real-time fluorescence detection. The latter was the most sensitive, detecting as little as 0.78 ng of pike DNA; the qPCR detection limit was 0.1 ng. The LAMP analysis took 20-70 min, which is significantly faster than qPCR. The study provides reliable detection and quantification of the parvalbumin gene in both fresh and processed samples and further highlights the versatility of the use of the parvalbumin gene for the authentication of food products and consumer protection via refined allergen risk assessment that is independent of the type of tissue or food processing method used.
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Affiliation(s)
- Eliška Čermáková
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Subham Mukherjee
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Lennard-Jones
School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Denisa Nováková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Petra Horká
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Kamila Zdeňková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Kateřina Demnerová
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
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2
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Potter BA, Halffman CM, McKinney HJ, Reuther JD, Finney BP, Lanoë FB, López JA, Holmes CE, Palmer E, Capps M, Kemp BM. Freshwater and anadromous fishing in Ice Age Beringia. SCIENCE ADVANCES 2023; 9:eadg6802. [PMID: 37267368 PMCID: PMC10413661 DOI: 10.1126/sciadv.adg6802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/01/2023] [Indexed: 06/04/2023]
Abstract
While freshwater and anadromous fish have been critical economic resources for late prehistoric and modern Native Americans, the origin and development of fishing is not well understood. We document the earliest known human use of freshwater and anadromous fish in North America by 13,000 and 11,800 years ago, respectively, from primary anthropogenic contexts in central Alaska (eastern Beringia). Fish use appears conditioned by broad climatic factors, as all occurrences but one are within the Younger Dryas chronozone. Earlier Bølling-Allerød and later early Holocene components, while exhibiting similar organic preservation, did not yield evidence of fishing, suggesting that this was a response to changing environmental factors, perhaps reductions in higher ranked resources such as large terrestrial mammals. Late Pleistocene and recent Indigenous peoples harvested similar fish taxa in the region (salmon, burbot, whitefish, and pike). We characterize late Pleistocene fishing in interior Beringia as an important element of broad-spectrum foraging rather than the intensive communal fishing and storage common among recent peoples.
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Affiliation(s)
- Ben A. Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Carrin M. Halffman
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Holly J. McKinney
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Joshua D. Reuther
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Bruce P. Finney
- Department of Biological Sciences and Geosciences, Idaho State University, Pocatello, ID, USA
| | - François B. Lanoë
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
- Bureau of Applied Research in Anthropology, University of Arizona, Tucson AZ, USA
| | - J. Andrés López
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
- Department of Fishes and Marine Invertebrates, University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Charles E. Holmes
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Erica Palmer
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
| | - Marie Capps
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
| | - Brian M. Kemp
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
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3
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Campbell MA, Hale MC, Jalbert CS, Dunker K, Sepulveda AJ, López JA, Falke JA, Westley PAH. Genomics reveal the origins and current structure of a genetically depauperate freshwater species in its introduced Alaskan range. Evol Appl 2023; 16:1119-1134. [PMID: 37360023 PMCID: PMC10286226 DOI: 10.1111/eva.13556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 06/28/2023] Open
Abstract
Invasive species are a major threat to global biodiversity, yet also represent large-scale unplanned ecological and evolutionary experiments to address fundamental questions in nature. Here we analyzed both native and invasive populations of predatory northern pike (Esox lucius) to characterize landscape genetic variation, determine the most likely origins of introduced populations, and investigate a presumably postglacial population from Southeast Alaska of unclear provenance. Using a set of 4329 SNPs from 351 individual Alaskan northern pike representing the most widespread geographic sampling to date, our results confirm low levels of genetic diversity in native populations (average 𝝅 of 3.18 × 10-4) and even less in invasive populations (average 𝝅 of 2.68 × 10-4) consistent with bottleneck effects. Our analyses indicate that invasive northern pike likely came from multiple introductions from different native Alaskan populations and subsequently dispersed from original introduction sites. At the broadest scale, invasive populations appear to have been founded from two distinct regions of Alaska, indicative of two independent introduction events. Genetic admixture resulting from introductions from multiple source populations may have mitigated the negative effects associated with genetic bottlenecks in this species with naturally low levels of genetic diversity. Genomic signatures strongly suggest an excess of rare, population-specific alleles, pointing to a small number of founding individuals in both native and introduced populations consistent with a species' life history of limited dispersal and gene flow. Lastly, the results strongly suggest that a small isolated population of pike, located in Southeast Alaska, is native in origin rather than stemming from a contemporary introduction event. Although theory predicts that lack of genetic variation may limit colonization success of novel environments, we detected no evidence that a lack of standing variation limited the success of this genetically depauperate apex predator.
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Affiliation(s)
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Chase S. Jalbert
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksFairbanksAlaskaUSA
- Present address:
Division of Commercial FisheriesAlaska Department of Fish and GameAnchorageAlaskaUSA
| | - Kristine Dunker
- Division of Sport FishAlaska Department of Fish and GameAnchorageAlaskaUSA
| | - Adam J. Sepulveda
- Northern Rocky Mountain Science CenterU.S. Geological SurveyBozemanMontanaUSA
| | - J. Andrés López
- University of Alaska MuseumFairbanksAlaskaUSA
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Jeffrey A. Falke
- Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological SurveyUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Peter A. H. Westley
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksFairbanksAlaskaUSA
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Appraising the Genetic Makeup of an Allochthonous Southern Pike Population: An Opportunity to Predict the Evolution of Introgressive Hybridization in Isolated Populations? Animals (Basel) 2023; 13:ani13030380. [PMID: 36766269 PMCID: PMC9913590 DOI: 10.3390/ani13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Biological invasions are a major threat to the conservation of biodiversity, as invasive species affect native biota through competition, predation, pathogen introduction, habitat alteration, and hybridisation. The present study focuses on a southern pike population, Esox cisalpinus (Teleostei: Esocidae), that has been introduced outside the species' native range. Using microsatellite markers, this study's objective was to gather baseline genetic information and assess the presence of hybrids between this species and E. lucius in the introduced population. The resulting estimates of genetic diversity and effective population size are comparable to those observed in the species' native range. Although different methods yield contrasting and uncertain evidence regarding introgressive hybridization, the presence of late-generation hybrids cannot be completely ruled out. Large numbers of breeders as well as multiple introductions of genetically divergent cohorts and introgressive hybridisation may explain the high genetic diversity of this recently introduced southern pike population. The present study issues a warning that the conservation of southern pike' introgressive hybridisation between northern and southern pike might be underestimated. The genetic information gathered herein may unravel the origin, number of introduction events, and evolutionary trajectory of the introduced population. This information may help us understand the evolution of introgressive hybridisation in the southern pike's native areas.
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A new species of Myxidium (Cnidaria: Myxosporea: Myxidiidae) from the gallbladder of pickerels, Esox spp. (Esociformes: Esocidae), from southwestern Arkansas, USA. Syst Parasitol 2022; 99:611-620. [PMID: 35778584 DOI: 10.1007/s11230-022-10050-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
During April 2016 and again in November 2021, four Chain Pickerels, Esox niger were collected from Union (n = 3) and Nevada (n = 1) counties, Arkansas, USA, and 65 Grass Pickerels, Esox americanus vermiculatus were collected between January 2015 and December 2021 from four counties of Arkansas (n = 31) and McCurtain County, Oklahoma, USA (n = 34), and examined for myxozoans. Gallbladders of an individual E. niger from Nevada County, Arkansas, as well as a single individual of E. a. vermiculatus from Sevier County, Arkansas, were infected with a new myxozoan, Myxidium whippsi n. sp. Qualitative and quantitative morphological data were from formalin-fixed preserved myxospores while molecular data (SSU rRNA gene) consisted of 2031bp (host: E. niger) and 1723 bp (host: E. a. vermiculatus) partial sequences of the small subunit ribosomal RNA gene. Phylogenetic analysis placed M. whippsi n. sp. in a clade with two other myxozoans, Zschokkella nova and Myxidium truttae, previously reported from cyprinids and salmonids, respectively. We document the first report of a myxozoan from E. a. vermiculatus. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:A50FCEB3-68C3-428E-A04E-37A16790F1EB.
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6
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Takács P, Bánó B, Czeglédi I, Erős T, Ferincz Á, Gál B, Bánó-Kern B, Kovács B, Nagy AA, Nyeste K, Lente V, Preiszner B, Sipos S, Staszny Á, Vitál Z, Weiperth A, Csoma E. The mixed phylogenetic origin of northern pike (Esox lucius Linnaeus 1758) populations in the Middle Danubian drainage. BMC ZOOL 2022; 7:28. [PMID: 37170181 PMCID: PMC10127386 DOI: 10.1186/s40850-022-00129-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pikes, members of genus Esox, are widespread freshwater predators of the northern hemisphere, and important sport fish also. From the Carpathian basin only one species, the northern pike (E. lucius) is noted. At the same time the pike stocks living in this area show high level of phenotypic variance (e.g. various body pattern) and its growth varies highly both among and within populations. These features usually explained by the environmental diversity of the area. Whereas we think that genetic reasons -e.g. the appearance of other/new pike species in the area- may also be responsible for these observed features. Since as no detailed information have been published from the pike populations of this area, so far; we conducted phylogenetic and morphological assay on 88 pike specimens, collected from 49 Middle Danubian sampling sites. RESULTS Our phylogenetic surveys showed that the northern pike appear in the study area solely, but all the three of its major lineages (Northern, Circumpolar, Southern) were indicated. Only six specimens represent the Northern lineage, collected from the western part of the study area. The Circumpolar and Southern lineages were common in the Carpathian basin, but the Southern lineage showed higher levels of haplotype diversity than the Circumpolar clade. Which indicates that only the Southern lineage is native in the area, while the other two groups could have appeared in the Middle Danubian system either spontaneously or by human introduction. Moreover, the different clades appeared in the same populations, suggesting the opportunity of inter-lineage hybridisation. From the studied morphologicalal features, the number of scales on the lateral line and the head length showed significant differences among the lineages. At the same time the body pattern of the studied individuals seems to be rather influenced by the ontogenic changes than phylogeny. CONCLUSIONS The high phenotypic variability of Middle Danubian northern pike populations may be due that all of its three major clades appeared and came in secondary contact in the area. In the within watershed spread of the non-native lineages the human stocking/transfer may play a considerable role.
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Affiliation(s)
- Péter Takács
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary.
| | - Bálint Bánó
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - István Czeglédi
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Tibor Erős
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Árpád Ferincz
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Blanka Gál
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Bernadett Bánó-Kern
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - András Attila Nagy
- "MilvusGroup" Birdland Nature Protection Association, Crinului nr 22, 540343, Tîrgu Mureș, Romania
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, University Babeş-Bolyai, Strada Clinicilor 5-7, 400006, Cluj-Napoca-Napoca, Romania
| | - Krisztián Nyeste
- Department of Hydrobiology, Faculty of Science and Technology, University of Debrecen, Egyetem sqr. 1, Debrecen, 4032, Hungary
| | - Vera Lente
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Bálint Preiszner
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Sándor Sipos
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21102, Novi Sad, Serbia
| | - Ádám Staszny
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Zoltán Vitál
- Research Center for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Anna-liget u. 35, Szarvas, 5540, Hungary
| | - András Weiperth
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Eszter Csoma
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, 4032, Hungary
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7
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Sunde J, Yıldırım Y, Tibblin P, Bekkevold D, Skov C, Nordahl O, Larsson P, Forsman A. Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments. Mol Ecol 2021; 31:1093-1110. [PMID: 34874594 DOI: 10.1111/mec.16315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/28/2023]
Abstract
Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.
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Affiliation(s)
- Johanna Sunde
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Christian Skov
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Oscar Nordahl
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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8
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Hierarchical genetic structure and implications for conservation of the world's largest salmonid, Hucho taimen. Sci Rep 2021; 11:20508. [PMID: 34654859 PMCID: PMC8520000 DOI: 10.1038/s41598-021-99530-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.
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9
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Lehmann R, Kovařík A, Ocalewicz K, Kirtiklis L, Zuccolo A, Tegner JN, Wanzenböck J, Bernatchez L, Lamatsch DK, Symonová R. DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows. Genome Biol Evol 2021; 13:6380143. [PMID: 34599322 PMCID: PMC8557787 DOI: 10.1093/gbe/evab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Genome sizes of eukaryotic organisms vary substantially, with whole-genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and Umbra pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5 and 5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in U. limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.
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Affiliation(s)
- Robert Lehmann
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Science, Brno, Czech Republic
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Gdansk, Poland
| | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jesper N Tegner
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Josef Wanzenböck
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Louis Bernatchez
- Department of Biology, IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
| | - Dunja K Lamatsch
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,Department of Biology, Faculty of Biology, University of Hradec Kralove, Czech Republic
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10
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Pan Q, Feron R, Jouanno E, Darras H, Herpin A, Koop B, Rondeau E, Goetz FW, Larson WA, Bernatchez L, Tringali M, Curran SS, Saillant E, Denys GPJ, von Hippel FA, Chen S, López JA, Verreycken H, Ocalewicz K, Guyomard R, Eche C, Lluch J, Roques C, Hu H, Tabor R, DeHaan P, Nichols KM, Journot L, Parrinello H, Klopp C, Interesova EA, Trifonov V, Schartl M, Postlethwait J, Guiguen Y. The rise and fall of the ancient northern pike master sex-determining gene. eLife 2021; 10:e62858. [PMID: 33506762 PMCID: PMC7870143 DOI: 10.7554/elife.62858] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
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Affiliation(s)
- Qiaowei Pan
- INRAE, LPGPRennesFrance
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Romain Feron
- INRAE, LPGPRennesFrance
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Hugo Darras
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | | | - Ben Koop
- Department of Biology, Centre for Biomedical Research, University of VictoriaVictoriaCanada
| | - Eric Rondeau
- Department of Biology, Centre for Biomedical Research, University of VictoriaVictoriaCanada
| | - Frederick W Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAASeattleUnited States
| | - Wesley A Larson
- Fisheries Aquatic Science and Technology Laboratory at Alaska Pacific UniversityAnchorageUnited States
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
| | - Mike Tringali
- Fish and Wildlife Conservation Commission, Florida Marine Research InstituteSt. PetersburgUnited States
| | - Stephen S Curran
- School of Fisheries and Aquatic Sciences, Auburn UniversityAuburnUnited States
| | - Eric Saillant
- Gulf Coast Research Laboratory, School of Ocean Science and Technology, The University of Southern MississippiOcean SpringsUnited States
| | - Gael PJ Denys
- Laboratoire de Biologie des organismes et écosystèmes aquatiques (BOREA), MNHN, CNRS, IRD, SU, UCN, Laboratoire de Biologie des organismes et écosystèmes aquatiques (BOREA)ParisFrance
- Unité Mixte de Service Patrimoine Naturelle – Centre d’expertise et de données (UMS 2006 AFB, CNRS, MNHN), Muséum national d’Histoire naturelleParisFrance
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona UniversityFlagstaffUnited States
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, CAFS, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao)QingdaoChina
| | - J Andrés López
- College of Fisheries and Ocean Sciences FisheriesFairbanksUnited States
| | - Hugo Verreycken
- Research Institute for Nature and Forest (INBO)BrusselsBelgium
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, University of GdanskGdanskPoland
| | | | - Camille Eche
- GeT‐PlaGe, INRAE, GenotoulCastanet-TolosanFrance
| | - Jerome Lluch
- GeT‐PlaGe, INRAE, GenotoulCastanet-TolosanFrance
| | | | - Hongxia Hu
- Beijing Fisheries Research Institute & Beijing Key Laboratory of Fishery BiotechnologyBeijingChina
| | - Roger Tabor
- U.S. Fish and Wildlife ServiceLaceyUnited States
| | | | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattleUnited States
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. MontpellierMontpellierFrance
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. MontpellierMontpellierFrance
| | | | | | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State UniversityNovosibirskRussian Federation
| | - Manfred Schartl
- University of Wuerzburg, Developmental Biochemistry, Biocenter, 97074 Würzburg, Germany; and The Xiphophorus Genetic Stock Center, Texas State UniversitySan MarcosUnited States
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11
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Weiss SJ, Gonçalves DV, Secci-Petretto G, Englmaier GK, Gomes-Dos-Santos A, Denys GPJ, Persat H, Antonov A, Hahn C, Taylor EB, Froufe E. Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00468-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractGraylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.
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12
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Zangl L, Daill D, Gessl W, Friedrich T, Koblmüller S. Austrian gudgeons of the genusGobio(Teleostei: Gobionidae): A mixture of divergent lineages. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lukas Zangl
- Institute of Biology University of Graz Graz Austria
| | - Daniel Daill
- Institute of Biology University of Graz Graz Austria
- Consultants in Aquatic Ecology and Engineering –blattfisch e.U. Wels Austria
| | | | - Thomas Friedrich
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna Vienna Austria
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13
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Bachevskaja LT, Pereverzeva VV, Agapova GA, Grunin SI. Genetic Diversity of the Population of Northern Pike Esox lucius L. from the Rivers of the Northeastern Part of Russia. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019020031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Bolotov IN, Vikhrev IV, Bespalaya YV, Gofarov MY, Kondakov AV, Konopleva ES, Bolotov NN, Lyubas AA. Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida). Mol Phylogenet Evol 2016; 103:104-121. [DOI: 10.1016/j.ympev.2016.07.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 07/01/2016] [Accepted: 07/18/2016] [Indexed: 11/16/2022]
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15
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Goulet CL, Smith HJ, Maie T. Comparative lever analysis and ontogenetic scaling in esocid fishes: Functional demands and constraints in feeding biomechanics. J Morphol 2016; 277:1447-1458. [PMID: 27552975 DOI: 10.1002/jmor.20586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/14/2016] [Accepted: 07/23/2016] [Indexed: 11/07/2022]
Abstract
When animals grow, the functional demands that they experience often change as a consequence of their increasing body size. In this study, we examined the feeding biomechanics in esocid species that represent different size classes (small, Esox americanus; intermediate, Esox niger; large, Esox lucius), and how their bite forces and associated functional variables change as they grow. In order to evaluate bite performance through ontogeny, we dissected and measured dimensions of the feeding apparatus and the adductor mandibulae muscle complex with its segmentum facialis subdivisions such as the ricto-malaris, stegalis and endoricto-malaris across a wide range of body sizes. The collected morphological data was used as input variables for a published anatomical model to simulate jaw function in these fish species. Maximum bite forces for both anterior bite and posterior bite increased in isometry in E. americanus and E. niger. The posterior bite of E. lucius also increases in isometry, however, the anterior bite increases in positive allometry. Intraspecific comparison within E. lucius indicated the increase of bite forces in more developed individuals accelerated after the fish grew out of fingerling stage. In addition, our analysis indicated functional differentiation between subdivisions of the adductor mandibulae segmentum facialis, as well as interspecific differences in the pattern of contribution to the bite performance by these subdivisions. Our study provides insights into not only the musculoskeletal basis of the jaw function of esocid species, but also the feeding capacity of this species in relation to the functional demands it faces as one of the top predators in lake and river systems. J. Morphol. 277:1447-1458, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Courtney L Goulet
- Department of Biological Sciences, St. Cloud State University, Wick Science Building, 720 Fourth Avenue South, St. Cloud, Minnesota, 56301
| | - Harrison J Smith
- Department of Biology, Lynchburg College, 225 Hobbs-Sigler Hall, School of Science, 1501 Lakeside Drive, Lynchburg, Virginia, 24501
| | - Takashi Maie
- Department of Biology, Lynchburg College, 225 Hobbs-Sigler Hall, School of Science, 1501 Lakeside Drive, Lynchburg, Virginia, 24501.
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16
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Takahashi H, Møller PR, Shedko SV, Ramatulla T, Joen SR, Zhang CG, Sideleva VG, Takata K, Sakai H, Goto A, Nishida M. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers. Mol Phylogenet Evol 2016; 99:44-52. [DOI: 10.1016/j.ympev.2016.03.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
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